import jalview.datamodel.SequenceI;
import java.util.Arrays;
+import java.util.Collections;
+import java.util.Comparator;
import java.util.List;
import java.util.Map;
import java.util.Vector;
+/**
+ * A helper class to parse URL Link strings taken from applet parameters or
+ * jalview properties file using the com.stevesoft.pat.Regex implementation.
+ * Jalview 2.4 extension allows regular expressions to be used to parse ID
+ * strings and replace the result in the URL. Regex's operate on the whole ID
+ * string given to the matchURL method, if no regex is supplied, then only text
+ * following the first pipe symbol will be substituted. Usage documentation
+ * todo.
+ */
public class UrlLink
{
+ private static final String SEQUENCEID_PLACEHOLDER = DELIM + SEQUENCE_ID
+ + DELIM;
+
+ private static final String ACCESSION_PLACEHOLDER = DELIM + DB_ACCESSION
+ + DELIM;
+
/**
- * helper class to parse URL Link strings taken from applet parameters or
- * jalview properties file using the com.stevesoft.pat.Regex implementation.
- * Jalview 2.4 extension allows regular expressions to be used to parse ID
- * strings and replace the result in the URL. Regex's operate on the whole ID
- * string given to the matchURL method, if no regex is supplied, then only
- * text following the first pipe symbol will be substituted. Usage
- * documentation todo.
+ * A comparator that puts SEQUENCE_ID template links before DB_ACCESSION
+ * links, and otherwise orders by link name + url (not case sensitive). It
+ * expects to compare strings formatted as "Name|URLTemplate" where the
+ * template may include $SEQUENCE_ID$ or $DB_ACCESSION$ or neither.
*/
+ public static final Comparator<String> LINK_COMPARATOR = new Comparator<String>()
+ {
+ @Override
+ public int compare(String link1, String link2)
+ {
+ if (link1 == null || link2 == null)
+ {
+ return 0; // for failsafe only
+ }
+ if (link1.contains(SEQUENCEID_PLACEHOLDER)
+ && link2.contains(ACCESSION_PLACEHOLDER))
+ {
+ return -1;
+ }
+ if (link2.contains(SEQUENCEID_PLACEHOLDER)
+ && link1.contains(ACCESSION_PLACEHOLDER))
+ {
+ return 1;
+ }
+ return String.CASE_INSENSITIVE_ORDER.compare(link1, link2);
+ }
+ };
private static final String EQUALS = "=";
String var = (usesDBaccession ? DB_ACCESSION : SEQUENCE_ID);
return urlPrefix
- + (dynamic ? (DELIM + var + ((regexReplace != null) ? EQUALS
- + regexReplace + EQUALS + DELIM : DELIM)) : "")
+ + (dynamic
+ ? (DELIM + var
+ + ((regexReplace != null)
+ ? EQUALS + regexReplace + EQUALS + DELIM
+ : DELIM))
+ : "")
+ ((urlSuffix == null) ? "" : urlSuffix);
}
{
if (regexReplace != null)
{
- com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex.perlCode("/"
- + regexReplace + "/");
+ com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex
+ .perlCode("/" + regexReplace + "/");
if (rg.search(idstring))
{
int ns = rg.numSubs();
+ rg.stringMatched(s) + "'");
}
// try to collate subgroup matches
- Vector<String> subs = new Vector<String>();
+ Vector<String> subs = new Vector<>();
// have to loop through submatches, collating them at top level
// match
int s = 0; // 1;
if (rg.matchedFrom(s) > -1)
{
subs.addElement(rg.stringMatched(s));
- subs.addElement(urlPrefix + rg.stringMatched(s)
- + urlSuffix);
+ subs.addElement(
+ urlPrefix + rg.stringMatched(s) + urlSuffix);
}
s++;
}
regexReplace = link.substring(sqidPos + startLength, p);
try
{
- com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex.perlCode("/"
- + regexReplace + "/");
+ com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex
+ .perlCode("/" + regexReplace + "/");
if (rg == null)
{
invalidMessage = "Invalid Regular Expression : '" + regexReplace
if (usesDBAccession()) // link is ID
{
// collect matching db-refs
- DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
- new String[] { target });
+ List<DBRefEntry> dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
+ new String[]
+ { target });
// if there are any dbrefs which match up with the link
if (dbr != null)
{
- for (int r = 0; r < dbr.length; r++)
+ for (int r = 0, nd = dbr.size(); r < nd; r++)
{
// create Bare ID link for this URL
- createBareURLLink(dbr[r].getAccessionId(), true, linkset);
+ createBareURLLink(dbr.get(r).getAccessionId(), true, linkset);
}
}
}
}
}
}
+
+ /**
+ * Sorts links (formatted as LinkName|LinkPattern) suitable for display in a
+ * menu
+ * <ul>
+ * <li>SEQUENCE_ID links precede DB_ACCESSION links (i.e. canonical lookup
+ * before cross-references)</li>
+ * <li>otherwise by Link name (case insensitive)</li>
+ * </ul>
+ *
+ * @param nlinks
+ */
+ public static void sort(List<String> nlinks)
+ {
+ Collections.sort(nlinks, LINK_COMPARATOR);
+ }
}